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Lara-Gonzalez P, Variyar S, Moghareh S, Nguyen ACN, Kizhedathu A, Budrewicz J, Schlientz A, Varshney N, Bellaart A, Oegema K, Bardwell L, Desai A. Cyclin B3 is a dominant fast-acting cyclin that drives rapid early embryonic mitoses. J Cell Biol 2024; 223:e202308034. [PMID: 39105756 PMCID: PMC11303871 DOI: 10.1083/jcb.202308034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/27/2024] [Accepted: 07/18/2024] [Indexed: 08/07/2024] Open
Abstract
Mitosis in early embryos often proceeds at a rapid pace, but how this pace is achieved is not understood. Here, we show that cyclin B3 is the dominant driver of rapid embryonic mitoses in the C. elegans embryo. Cyclins B1 and B2 support slow mitosis (NEBD to anaphase ∼600 s), but the presence of cyclin B3 dominantly drives the approximately threefold faster mitosis observed in wildtype. Multiple mitotic events are slowed down in cyclin B1 and B2-driven mitosis, and cyclin B3-associated Cdk1 H1 kinase activity is ∼25-fold more active than cyclin B1-associated Cdk1. Addition of cyclin B1 to fast cyclin B3-only mitosis introduces an ∼60-s delay between completion of chromosome alignment and anaphase onset; this delay, which is important for segregation fidelity, is dependent on inhibitory phosphorylation of the anaphase activator Cdc20. Thus, cyclin B3 dominance, coupled to a cyclin B1-dependent delay that acts via Cdc20 phosphorylation, sets the rapid pace and ensures mitotic fidelity in the early C. elegans embryo.
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Affiliation(s)
- Pablo Lara-Gonzalez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Ludwig Institute for Cancer Research , La Jolla, CA, USA
| | - Smriti Variyar
- Department of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Shabnam Moghareh
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Anh Cao Ngoc Nguyen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Amrutha Kizhedathu
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | | | - Aleesa Schlientz
- Department of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Neha Varshney
- Department of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Andrew Bellaart
- Department of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Karen Oegema
- Ludwig Institute for Cancer Research , La Jolla, CA, USA
- Department of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Lee Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Arshad Desai
- Ludwig Institute for Cancer Research , La Jolla, CA, USA
- Department of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
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2
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Van Matre S, Huq S, Akana L, Eldridge DE, Zuniga O, Rodrigues H, Wolfe AR. Enhanced radiosensitivity of pancreatic cancer achieved through inhibition of Cyclin-dependent kinase 1. Radiother Oncol 2024; 200:110531. [PMID: 39270987 DOI: 10.1016/j.radonc.2024.110531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 09/04/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND AND PURPOSE Overcoming radioresistance is a critical challenge in pancreatic ductal adenocarcinoma (PDAC). Our study investigates the targeting of Cyclin-dependent kinase-1 (CDK1) through genetic and pharmaceutical inhibition to radiosensitize PDAC cells. MATERIALS AND METHODS Mass spectrometry and phosphoproteomics were used to analyze engineered radiation-resistant PDAC cell lines (MIA PaCa-2 and PANC-1) compared to parental controls. The TCGA PDAC database was queried for clinical outcomes and patients were dichotomized based on the median CDK1 mRNA expression. We generated a microRNA-based TET-on inducible shRNA to inhibit CDK1 expression in two PDAC cell lines. We used an orthotopic model of PDAC to test the radiation sensitivity of PDAC tumors with or without doxycycline treatment. We targeted CDK1 activation with a selective CDK1 inhibitor, RO-3306, followed by in vitro experiments employing immunoblotting, immunocytochemistry, and clonogenic assays. RESULTS Phosphoproteomics analysis revealed that phospho-CDK1 (Tyr15) was significantly elevated in the resistant clones. We found that high CDK1 expression was associated with worse OS in PDAC patients. Radiation exposure increased CDK1 phosphorylation. In MIA PaCa-2 and PANC-1 cells, CDK1 inhibition synergized with radiation therapy to delay tumor growth in vivo. CDK1 inhibition via. RO-3306 resulted in a significant shift of cells into the G2/M phase and disrupted DNA repair after radiation exposure. In vitro, pre-treatment with RO-3306 led to enhanced radiosensitivity of PDAC cells. CONCLUSION CDK1 plays a crucial role in PDAC radioresistance. Targeting CDK1 with radiotherapy holds promise for further investigation in PDAC treatment.
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Affiliation(s)
- Stetson Van Matre
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Saaimatul Huq
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Lokesh Akana
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Daniel E Eldridge
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Oscar Zuniga
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Henrique Rodrigues
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Adam R Wolfe
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States.
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Liu J, Li Q, Wang J, Qiu J, Zhou J, Peng Q. Genetically Encoded Fluorescence Resonance Energy Transfer Biosensor for Live-Cell Visualization of Lamin A Phosphorylation at Serine 22. Biomater Res 2024; 28:0091. [PMID: 39440272 PMCID: PMC11494032 DOI: 10.34133/bmr.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 09/05/2024] [Accepted: 09/24/2024] [Indexed: 10/25/2024] Open
Abstract
Extensive phosphorylation at serine 22 (pSer22) on lamin A is the hallmark of cell mitosis, which contributes to the breakdown of nuclear envelope. In the interphase, pSer22 lamin A exists in low abundance and is involved in mechanotransduction, virus infection, and gene expression. Numerous evidences emerge to support lamin A regulation on cell function and fate by phosphorylation. However, live-cell imaging tools for visualizing the dynamics of pSer22 lamin A are yet to be established. Herein, we developed a novel lamin A phosphorylation sensor (LAPS) based on fluorescence resonance energy transfer (FRET) with high sensitivity and specificity. We observed the dynamic lamin A phosphorylation during the cell cycle progression in single living cells: the increase of pSer22 modification when cells entered the mitosis and recovered upon the mitosis exit. Our biosensor also showed the gradual reduction of pSer22 modification during cell adhesion and in response to hypotonic environment. By applying LAPS, we captured the propagation of pSer22 modification from inside to outside of the inner nuclear membrane, which further led to the breakdown of nuclear envelope. Meanwhile, we found the synchronous phosphorylation of pSer22 lamin A and H3S10ph at mitosis entry. Inhibition of Aurora B, the responsible kinase for H3S10ph, could shorten the mitotic period without obvious effect on the pSer22 modification level of lamin A. Thus, LAPS allows the spatiotemporal visualization of the lamin A pSer22, which will be useful for elucidating the molecular mechanisms underlying cell mitosis and mechanoresponsive processes.
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Affiliation(s)
- Jian Liu
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Qianqian Li
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | | | - Juhui Qiu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, College of Bioengineering,
Chongqing University, Chongqing 400030, China
| | - Jing Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Department of Cardiology,
Peking University Third Hospital, National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing 100191, China
| | - Qin Peng
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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4
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Polito MP, Romaldini A, Tagliazucchi L, Marini G, Radice F, Gozza GA, Bergamini G, Costi MP, Enzo E. Biochemical characterization of the feedforward loop between CDK1 and FOXM1 in epidermal stem cells. Biol Direct 2024; 19:91. [PMID: 39396994 PMCID: PMC11472434 DOI: 10.1186/s13062-024-00540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Accepted: 10/07/2024] [Indexed: 10/15/2024] Open
Abstract
The complex network governing self-renewal in epidermal stem cells (EPSCs) is only partially defined. FOXM1 is one of the main players in this network, but the upstream signals regulating its activity remain to be elucidated. In this study, we identify cyclin-dependent kinase 1 (CDK1) as the principal kinase controlling FOXM1 activity in human primary keratinocytes. Mass spectrometry identified CDK1 as a key hub in a stem cell-associated protein network, showing its upregulation and interaction with essential self renewal-related markers. CDK1 phosphorylates FOXM1 at specific residues, stabilizing the protein and enhancing its nuclear localization and transcriptional activity, promoting self-renewal. Additionally, FOXM1 binds to the CDK1 promoter, inducing its expression.We identify the CDK1-FOXM1 feedforward loop as a critical axis sustaining EPSCs during in vitro cultivation. Understanding the upstream regulators of FOXM1 activity offers new insights into the biochemical mechanisms underlying self-renewal and differentiation in human primary keratinocytes.
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Affiliation(s)
- Maria Pia Polito
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Via Glauco Gottardi 100, Modena, Italy
| | - Alessio Romaldini
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Via Glauco Gottardi 100, Modena, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, Modena, 41125, Italy
| | - Grazia Marini
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Via Glauco Gottardi 100, Modena, Italy
| | - Federica Radice
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Via Glauco Gottardi 100, Modena, Italy
| | - Gaia Andrea Gozza
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Via Glauco Gottardi 100, Modena, Italy
| | - Giulia Bergamini
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Via Glauco Gottardi 100, Modena, Italy
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, Modena, 41125, Italy
| | - Elena Enzo
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Via Glauco Gottardi 100, Modena, Italy.
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5
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Song G, Liu J, Tang X, Zhong J, Zeng Y, Zhang X, Zhou J, Zhou J, Cao L, Zhang Q, Li Y. Cell cycle checkpoint revolution: targeted therapies in the fight against malignant tumors. Front Pharmacol 2024; 15:1459057. [PMID: 39464635 PMCID: PMC11505109 DOI: 10.3389/fphar.2024.1459057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/16/2024] [Indexed: 10/29/2024] Open
Abstract
Malignant tumors are among the most important causes of death worldwide. The pathogenesis of a malignant tumor is complex and has not been fully elucidated. Studies have shown that such pathogenesis is related to abnormal cell cycle progression. The expression levels of cyclins, cyclin-dependent kinases (CDKs), and CDK inhibitors as well as functions of the cell cycle checkpoints determine whether the cell cycle progression is smooth. Cell-cycle-targeting drugs have the advantages of high specificity, low toxicity, low side effects, and low drug resistance. Identifying drugs that target the cell cycle and applying them in clinical treatments are expected to promote chemotherapeutic developments against malignant tumors. This article aims to review drugs targeted against the cell cycle and their action mechanisms.
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Affiliation(s)
- Guangming Song
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jue Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xing Tang
- Department of Assisted Reproductive Centre, The affiliated Zhuzhou hospital Xiangya medical college, Central South University, Zhuzhou, Hunan, China
| | - Jie Zhong
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yuhuan Zeng
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaodi Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jianbin Zhou
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jie Zhou
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Lu Cao
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Qunfeng Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yukun Li
- Department of Assisted Reproductive Centre, The affiliated Zhuzhou hospital Xiangya medical college, Central South University, Zhuzhou, Hunan, China
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6
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Chen Z, Wang X, Gao X, Arslanovic N, Chen K, Tyler JK. Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression. eLife 2024; 13:RP94001. [PMID: 39392398 PMCID: PMC11469672 DOI: 10.7554/elife.94001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024] Open
Abstract
In response to DNA double-strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and the identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR/Cas9 screen. Many of the top hits on our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G1 or G2 phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.
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Affiliation(s)
- Zulong Chen
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's HospitalBostonUnited States
- Department of Pediatrics, Harvard Medical SchoolBostonUnited States
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's HospitalBostonUnited States
- Department of Pediatrics, Harvard Medical SchoolBostonUnited States
| | - Nina Arslanovic
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's HospitalBostonUnited States
- Department of Pediatrics, Harvard Medical SchoolBostonUnited States
| | - Jessica K Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
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7
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Safieddine A, Benassy MN, Bonte T, Slimani F, Pourcelot O, Kress M, Ernoult-Lange M, Courel M, Coleno E, Imbert A, Laine A, Godebert AM, Vinit A, Blugeon C, Chevreux G, Gautheret D, Walter T, Bertrand E, Bénard M, Weil D. Cell-cycle-dependent mRNA localization in P-bodies. Mol Cell 2024:S1097-2765(24)00744-5. [PMID: 39368464 DOI: 10.1016/j.molcel.2024.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 07/05/2024] [Accepted: 09/10/2024] [Indexed: 10/07/2024]
Abstract
Understanding the dynamics of RNA targeting to membraneless organelles is essential to disentangle their functions. Here, we investigate how P-bodies (PBs) evolve during cell-cycle progression in HEK293 cells. PB purification across the cell cycle uncovers widespread changes in their RNA content, partly uncoupled from cell-cycle-dependent changes in RNA expression. Single-molecule fluorescence in situ hybridization (FISH) shows various mRNA localization patterns in PBs peaking in G1, S, or G2, with examples illustrating the timely capture of mRNAs in PBs when their encoded protein becomes dispensable. Rather than directly reflecting absence of translation, cyclic mRNA localization in PBs can be controlled by RBPs, such as HuR in G2, and by RNA features. Indeed, while PB mRNAs are AU rich at all cell-cycle phases, they are specifically longer in G1, possibly related to post-mitotic PB reassembly. Altogether, our study supports a model where PBs are more than a default location for excess untranslated mRNAs.
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Affiliation(s)
- Adham Safieddine
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Marie-Noëlle Benassy
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, 75005 Paris, France
| | - Thomas Bonte
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, 75006 Paris, France; Institut Curie, PSL University, 75005 Paris, France; INSERM, U900, 75005 Paris, France
| | - Floric Slimani
- Institut de Génétique Humaine, University of Montpellier, CNRS, 34090 Montpellier, France
| | - Oriane Pourcelot
- Institut de Génétique Humaine, University of Montpellier, CNRS, 34090 Montpellier, France
| | - Michel Kress
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, 75005 Paris, France
| | - Michèle Ernoult-Lange
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, 75005 Paris, France
| | - Maïté Courel
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, 75005 Paris, France
| | - Emeline Coleno
- Institut de Génétique Humaine, University of Montpellier, CNRS, 34090 Montpellier, France
| | - Arthur Imbert
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, 75006 Paris, France
| | - Antoine Laine
- Institute for Integrative Biology of the Cell, UMR 9198, CEA, CNRS, Université Paris-Saclay, 91190 Gif-Sur-Yvette, France
| | - Annie Munier Godebert
- Research Center Saint-Antoine (CRSA), CISA Flow Cytometry Facility, UMRS 938, Sorbonne University, F-75012 Paris, France
| | - Angelique Vinit
- Research Center Saint-Antoine (CRSA), CISA Flow Cytometry Facility, UMRS 938, Sorbonne University, F-75012 Paris, France
| | - Corinne Blugeon
- GenomiqueENS, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Guillaume Chevreux
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, UMR 9198, CEA, CNRS, Université Paris-Saclay, 91190 Gif-Sur-Yvette, France
| | - Thomas Walter
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, 75006 Paris, France; Institut Curie, PSL University, 75005 Paris, France; INSERM, U900, 75005 Paris, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, University of Montpellier, CNRS, 34090 Montpellier, France
| | - Marianne Bénard
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, 75005 Paris, France
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, 75005 Paris, France.
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8
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Teotia V, Jha P, Chopra M. Discovery of Potential Inhibitors of CDK1 by Integrating Pharmacophore-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation Studies, and Evaluation of Their Inhibitory Activity. ACS OMEGA 2024; 9:39873-39892. [PMID: 39346877 PMCID: PMC11425824 DOI: 10.1021/acsomega.4c05414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 10/01/2024]
Abstract
The ability of CDK1 to compensate for the absence of other cell cycle CDKs poses a great challenge to treat cancers that overexpress these proteins. Despite several studies focusing on the area, there are no FDA-approved drugs selectively targeting CDK1. Here, the study aimed to develop potential CDK1 selective inhibitors through drug repurposing and leveraging the structural insights provided by the hit molecules generated. Approximately 280,000 compounds from DrugBank, Selleckchem, Otava and an in-house library were screened initially based on fit values using 3D QSAR pharmacophores built for CDK1 and subsequently through Lipinski, ADMET, and TOPKAT filters. 10,310 hits were investigated for docking into the binding site of CDK1 determined using the crystal structure of human CDK1 in complex with NU6102. The best 55 hits with better docking scores were further analyzed, and 12 hits were selected for 100 ns MD simulations followed by binding energy calculations using the MM-PBSA method. Finally, 10 hit molecules were tested in an in vitro CDK1 Kinase inhibition assay. Out of these, 3 hits showed significant CDK1 inhibitory potential with IC50 < 5 μM. These results indicate these compounds can be used to develop subtype-selective CDK1 inhibitors with better efficacy and reduced toxicities in the future.
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Affiliation(s)
- Vineeta Teotia
- Laboratory
of Molecular Modeling and Anti-Cancer Drug Development, Dr. B. R.
Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Prakash Jha
- Laboratory
of Molecular Modeling and Anti-Cancer Drug Development, Dr. B. R.
Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Madhu Chopra
- Laboratory
of Molecular Modeling and Anti-Cancer Drug Development, Dr. B. R.
Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
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9
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Majumdar S, Liu ST. Spatiotemporal regulation of MELK during mitosis. Front Cell Dev Biol 2024; 12:1406940. [PMID: 39355119 PMCID: PMC11443572 DOI: 10.3389/fcell.2024.1406940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 08/30/2024] [Indexed: 10/03/2024] Open
Abstract
Maternal Embryonic Leucine Zipper Kinase (MELK) has been studied intensively in recent years due to its overexpression in multiple cancers. However, the cell biology of MELK remains less characterized despite its well-documented association with mitosis. Here we report a distinctive pattern of human MELK that translocates from the cytoplasm to cell cortex within 3 min of anaphase onset. The cortex association lasts about 30 min till telophase. The spatiotemporal specific localization of MELK depends on the interaction between its Threonine-Proline (TP) rich domain and kinase associated 1 (KA1) domain, which is regulated by CDK1 kinase and PP4 protein phosphatase. KA1 domains are known to regulate kinase activities through various intramolecular interactions. Our results revealed a new role for KA1 domain to control subcellular localization of a protein kinase.
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Affiliation(s)
- Sreemita Majumdar
- Department of Biological Sciences, University of Toledo, Toledo, OH, United States
| | - Song-Tao Liu
- Department of Biological Sciences, University of Toledo, Toledo, OH, United States
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10
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Sarchi M, Clough CA, Crosse EI, Kim J, Baquero Galvis LD, Aydinyan N, Wellington R, Yang F, Gallì A, Creamer JP, Stewart S, Bradley RK, Malcovati L, Doulatov S. Mis-splicing of Mitotic Regulators Sensitizes SF3B1-Mutated Human HSCs to CHK1 Inhibition. Blood Cancer Discov 2024; 5:353-370. [PMID: 38856693 PMCID: PMC11369594 DOI: 10.1158/2643-3230.bcd-23-0230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/18/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024] Open
Abstract
Splicing factor SF3B1 mutations are frequent somatic lesions in myeloid neoplasms that transform hematopoietic stem cells (HSCs) by inducing mis-splicing of target genes. However, the molecular and functional consequences of SF3B1 mutations in human HSCs and progenitors (HSPCs) remain unclear. Here, we identify the mis-splicing program in human HSPCs as a targetable vulnerability by precise gene editing of SF3B1 K700E mutations in primary CD34+ cells. Mutant SF3B1 induced pervasive mis-splicing and reduced expression of genes regulating mitosis and genome maintenance leading to altered differentiation, delayed G2/M progression, and profound sensitivity to CHK1 inhibition (CHK1i). Mis-splicing or reduced expression of mitotic regulators BUBR1 and CDC27 delayed G2/M transit and promoted CHK1i sensitivity. Clinical CHK1i prexasertib selectively targeted SF3B1-mutant immunophenotypic HSCs and abrogated engraftment in vivo. These findings identify mis-splicing of mitotic regulators in SF3B1-mutant HSPCs as a targetable vulnerability engaged by pharmacological CHK1 inhibition. Significance: In this study, we engineer precise SF3B1 mutations in human HSPCs and identify CHK1 inhibition as a selective vulnerability promoted by mis-splicing of mitotic regulators. These findings uncover the mis-splicing program induced by mutant SF3B1 in human HSPCs and show that it can be therapeutically targeted by clinical CHK1 inhibitors.
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Affiliation(s)
- Martina Sarchi
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
| | - Courtnee A. Clough
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington.
| | - Edie I. Crosse
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington.
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington.
| | - Jason Kim
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Laura D. Baquero Galvis
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington.
| | - Nelli Aydinyan
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Rachel Wellington
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington.
| | - Feini Yang
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
| | - Anna Gallì
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, Pavia, Italy.
| | - J. Philip Creamer
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Sintra Stewart
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington.
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington.
- Department of Genome Sciences, University of Washington, Seattle, Washington.
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, Pavia, Italy.
| | - Sergei Doulatov
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, Washington.
- Department of Genome Sciences, University of Washington, Seattle, Washington.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.
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11
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Chen YL, Reddy S, Suzuki A. Reversible and effective cell cycle synchronization method for studying stage-specific investigations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.02.610832. [PMID: 39282459 PMCID: PMC11398389 DOI: 10.1101/2024.09.02.610832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The cell cycle is a crucial process for cell proliferation, differentiation, and development. Numerous genes and proteins play pivotal roles at specific cell cycle stages to regulate these events precisely. Studying the stage-specific functions of the cell cycle requires accumulating cell populations at the desired cell cycle stage. Cell synchronization, achieved through the use of cell cycle kinase and protein inhibitors, is often employed for this purpose. However, suboptimal concentrations of these inhibitors can result in reduced efficiency, irreversibility, and undesirable cell cycle defects. In this study, we have optimized effective and reversible techniques to synchronize the cell cycle at each stage in human RPE1 cells, utilizing both fixed high-precision cell cycle identification methods and high-temporal live-cell imaging. These reproducible synchronization methods are invaluable for investigating the regulatory mechanisms specific to each cell cycle stage.
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Affiliation(s)
- Yu-Lin Chen
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Syon Reddy
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Molecular and Cellular Pharmacology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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12
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Craig O, Lee S, Pilcher C, Saoud R, Abdirahman S, Salazar C, Williams N, Ascher D, Vary R, Luu J, Cowley K, Ramm S, Li MX, Thio N, Li J, Semple T, Simpson K, Gorringe K, Holien J. A new method for network bioinformatics identifies novel drug targets for mucinous ovarian carcinoma. NAR Genom Bioinform 2024; 6:lqae096. [PMID: 39184376 PMCID: PMC11344246 DOI: 10.1093/nargab/lqae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/11/2024] [Accepted: 07/23/2024] [Indexed: 08/27/2024] Open
Abstract
Mucinous ovarian carcinoma (MOC) is a subtype of ovarian cancer that is distinct from all other ovarian cancer subtypes and currently has no targeted therapies. To identify novel therapeutic targets, we developed and applied a new method of differential network analysis comparing MOC to benign mucinous tumours (in the absence of a known normal tissue of origin). This method mapped the protein-protein network in MOC and then utilised structural bioinformatics to prioritise the proteins identified as upregulated in the MOC network for their likelihood of being successfully drugged. Using this protein-protein interaction modelling, we identified the strongest 5 candidates, CDK1, CDC20, PRC1, CCNA2 and TRIP13, as structurally tractable to therapeutic targeting by small molecules. siRNA knockdown of these candidates performed in MOC and control normal fibroblast cell lines identified CDK1, CCNA2, PRC1 and CDC20, as potential drug targets in MOC. Three targets (TRIP13, CDC20, CDK1) were validated using known small molecule inhibitors. Our findings demonstrate the utility of our pipeline for identifying new targets and highlight potential new therapeutic options for MOC patients.
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Affiliation(s)
- Olivia Craig
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Samuel Lee
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Carlton, VIC 3010, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Courtney Pilcher
- School of Science, STEM College, RMIT University, Bundoora, VIC 3082, Australia
| | - Rita Saoud
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Suad Abdirahman
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Carolina Salazar
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Nathan Williams
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- School of Science, STEM College, RMIT University, Bundoora, VIC 3082, Australia
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4067, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Robert Vary
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Jennii Luu
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Karla J Cowley
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Susanne Ramm
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Mark Xiang Li
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Niko Thio
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
| | - Jason Li
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
| | - Tim Semple
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
| | - Kaylene J Simpson
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- The Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Jessica K Holien
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Carlton, VIC 3010, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
- School of Science, STEM College, RMIT University, Bundoora, VIC 3082, Australia
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13
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Fukuda N, Soga K, Taguchi C, Narushima J, Sakata K, Kato R, Yoshiba S, Shibata N, Kondo K. Cell cycle arrest combined with CDK1 inhibition suppresses genome-wide mutations by activating alternative DNA repair genes during genome editing. J Biol Chem 2024; 300:107695. [PMID: 39159810 PMCID: PMC11416245 DOI: 10.1016/j.jbc.2024.107695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 08/08/2024] [Accepted: 08/12/2024] [Indexed: 08/21/2024] Open
Abstract
Cells regularly repair numerous mutations. However, the effect of CRISPR/Cas9-induced dsDNA breaks on the repair processes of naturally occurring genome-wide mutations is unclear. In this study, we used TSCE5 cells with the heterozygous thymidine kinase genotype (TK+/-) to examine these effects. We strategically inserted the target sites for guide RNA (gRNA)/Cas9 and I-SceI into the functional allele and designed the experiment such that deletions of > 81 bp or base substitutions within exon five disrupted the TK gene, resulting in a TK-/- genotype. TSCE5 cells in the resting state exhibited 16 genome-wide mutations that affected cellular functions. After gRNA/Cas9 editing, these cells produced 859 mutations, including 67 high-impact variants that severely affected cellular functions under standard culture conditions. Mutation profile analysis indicated a significant accumulation of C to A substitutions, underscoring the widespread induction of characteristic mutations by gRNA/Cas9. In contrast, gRNA/Cas9-edited cells under conditions of S∼G2/M arrest and cyclin-dependent kinase 1 inhibition showed only five mutations. Transcriptomic analysis revealed the downregulation of DNA replication genes and upregulation of alternative DNA repair genes, such as zinc finger protein 384 (ZNF384) and dual specificity phosphatase, under S∼G2/M conditions. Additionally, activation of nucleotide and base excision repair gene, including O-6-methylguanine-DNA methyltransferase and xeroderma pigmentosum complementation group C, was observed. This study highlights the profound impact of CRISPR/Cas9 editing on genome-wide mutation processes and underscores the emergence of novel DNA repair pathways. Finally, our findings provide significant insights into the maintenance of genome integrity during genome editing.
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Affiliation(s)
- Nozomi Fukuda
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Keisuke Soga
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Chie Taguchi
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Jumpei Narushima
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kozue Sakata
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Reiko Kato
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoko Yoshiba
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Norihito Shibata
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kazunari Kondo
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan; Faculty of Food and Health Sciences, Showa Women's University, Tokyo, Japan.
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14
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Zheng XF, Sarkar A, Lotana H, Syed A, Nguyen H, Ivey RG, Kennedy JJ, Whiteaker JR, Tomasik B, Huang K, Li F, D'Andrea AD, Paulovich AG, Shah K, Spektor A, Chowdhury D. CDK5-cyclin B1 regulates mitotic fidelity. Nature 2024; 633:932-940. [PMID: 39232161 DOI: 10.1038/s41586-024-07888-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/30/2024] [Indexed: 09/06/2024]
Abstract
CDK1 has been known to be the sole cyclin-dependent kinase (CDK) partner of cyclin B1 to drive mitotic progression1. Here we demonstrate that CDK5 is active during mitosis and is necessary for maintaining mitotic fidelity. CDK5 is an atypical CDK owing to its high expression in post-mitotic neurons and activation by non-cyclin proteins p35 and p392. Here, using independent chemical genetic approaches, we specifically abrogated CDK5 activity during mitosis, and observed mitotic defects, nuclear atypia and substantial alterations in the mitotic phosphoproteome. Notably, cyclin B1 is a mitotic co-factor of CDK5. Computational modelling, comparison with experimentally derived structures of CDK-cyclin complexes and validation with mutational analysis indicate that CDK5-cyclin B1 can form a functional complex. Disruption of the CDK5-cyclin B1 complex phenocopies CDK5 abrogation in mitosis. Together, our results demonstrate that cyclin B1 partners with both CDK5 and CDK1, and CDK5-cyclin B1 functions as a canonical CDK-cyclin complex to ensure mitotic fidelity.
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Affiliation(s)
- Xiao-Feng Zheng
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aniruddha Sarkar
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Humphrey Lotana
- Department of Chemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Aleem Syed
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Huy Nguyen
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bartłomiej Tomasik
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Faculty of Medicine, Gdańsk, Poland
| | - Kaimeng Huang
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Feng Li
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D'Andrea
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kavita Shah
- Department of Chemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Alexander Spektor
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Dipanjan Chowdhury
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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15
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de la Cruz-Thea B, Natali L, Ho-Xuan H, Bruckmann A, Coll-Bonfill N, Strieder N, Peinado VI, Meister G, Musri MM. Differentiation and Growth-Arrest-Related lncRNA ( DAGAR): Initial Characterization in Human Smooth Muscle and Fibroblast Cells. Int J Mol Sci 2024; 25:9497. [PMID: 39273443 PMCID: PMC11394763 DOI: 10.3390/ijms25179497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
Vascular smooth muscle cells (SMCs) can transition between a quiescent contractile or "differentiated" phenotype and a "proliferative-dedifferentiated" phenotype in response to environmental cues, similar to what in occurs in the wound healing process observed in fibroblasts. When dysregulated, these processes contribute to the development of various lung and cardiovascular diseases such as Chronic Obstructive Pulmonary Disease (COPD). Long non-coding RNAs (lncRNAs) have emerged as key modulators of SMC differentiation and phenotypic changes. In this study, we examined the expression of lncRNAs in primary human pulmonary artery SMCs (hPASMCs) during cell-to-cell contact-induced SMC differentiation. We discovered a novel lncRNA, which we named Differentiation And Growth Arrest-Related lncRNA (DAGAR) that was significantly upregulated in the quiescent phenotype with respect to proliferative SMCs and in cell-cycle-arrested MRC5 lung fibroblasts. We demonstrated that DAGAR expression is essential for SMC quiescence and its knockdown hinders SMC differentiation. The treatment of quiescent SMCs with the pro-inflammatory cytokine Tumor Necrosis Factor (TNF), a known inducer of SMC dedifferentiation and proliferation, elicited DAGAR downregulation. Consistent with this, we observed diminished DAGAR expression in pulmonary arteries from COPD patients compared to non-smoker controls. Through pulldown experiments followed by mass spectrometry analysis, we identified several proteins that interact with DAGAR that are related to cell differentiation, the cell cycle, cytoskeleton organization, iron metabolism, and the N-6-Methyladenosine (m6A) machinery. In conclusion, our findings highlight DAGAR as a novel lncRNA that plays a crucial role in the regulation of cell proliferation and SMC differentiation. This paper underscores the potential significance of DAGAR in SMC and fibroblast physiology in health and disease.
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MESH Headings
- Humans
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Fibroblasts/metabolism
- Cell Differentiation/genetics
- Myocytes, Smooth Muscle/metabolism
- Cell Proliferation/genetics
- Pulmonary Artery/metabolism
- Pulmonary Artery/cytology
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/cytology
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/pathology
- Cells, Cultured
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Affiliation(s)
- Benjamin de la Cruz-Thea
- Mercedes and Martin Ferreyra Medical Research Institute, National Council for Scientific and Technical Research, National University of Córdoba (INIMEC-CONICET-UNC), Córdoba 5016, Argentina
| | - Lautaro Natali
- Mercedes and Martin Ferreyra Medical Research Institute, National Council for Scientific and Technical Research, National University of Córdoba (INIMEC-CONICET-UNC), Córdoba 5016, Argentina
| | - Hung Ho-Xuan
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Núria Coll-Bonfill
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Nicholas Strieder
- NGS-Core, LIT-Leibniz-Institute for Immunotherapy, 93053 Regensburg, Germany
| | - Víctor I Peinado
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona (IIBB), CSIC, 08036 Barcelona, Spain
- Department of Pulmonary Medicine, Hospital Clínic, Biomedical Research Institut August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Melina M Musri
- Mercedes and Martin Ferreyra Medical Research Institute, National Council for Scientific and Technical Research, National University of Córdoba (INIMEC-CONICET-UNC), Córdoba 5016, Argentina
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16
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Joshi JN, Lerner AD, Scallo F, Grumet AN, Matteson P, Millonig JH, Valvezan AJ. mTORC1 activity oscillates throughout the cell cycle, promoting mitotic entry and differentially influencing autophagy induction. Cell Rep 2024; 43:114543. [PMID: 39067023 DOI: 10.1016/j.celrep.2024.114543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/07/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024] Open
Abstract
Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a master metabolic regulator that is active in nearly all proliferating eukaryotic cells; however, it is unclear whether mTORC1 activity changes throughout the cell cycle. We find that mTORC1 activity oscillates from lowest in mitosis/G1 to highest in S/G2. The interphase oscillation is mediated through the TSC complex but is independent of major known regulatory inputs, including Akt and Mek/Erk signaling. By contrast, suppression of mTORC1 activity in mitosis does not require the TSC complex. mTORC1 has long been known to promote progression through G1. We find that mTORC1 also promotes progression through S and G2 and is important for satisfying the Chk1/Wee1-dependent G2/M checkpoint to allow entry into mitosis. We also find that low mTORC1 activity in G1 sensitizes cells to autophagy induction in response to partial mTORC1 inhibition or reduced nutrient levels. Together, these findings demonstrate that mTORC1 is differentially regulated throughout the cell cycle, with important phase-specific consequences for proliferating cells.
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Affiliation(s)
- Jay N Joshi
- Molecular Biosciences Program, Rutgers University, Piscataway, NJ, USA; Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - Ariel D Lerner
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - Frank Scallo
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | | | - Paul Matteson
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - James H Millonig
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA; Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Alexander J Valvezan
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA; Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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17
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Hibino K, Sakai Y, Tamura S, Takagi M, Minami K, Natsume T, Shimazoe MA, Kanemaki MT, Imamoto N, Maeshima K. Single-nucleosome imaging unveils that condensins and nucleosome-nucleosome interactions differentially constrain chromatin to organize mitotic chromosomes. Nat Commun 2024; 15:7152. [PMID: 39169041 PMCID: PMC11339268 DOI: 10.1038/s41467-024-51454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
For accurate mitotic cell division, replicated chromatin must be assembled into chromosomes and faithfully segregated into daughter cells. While protein factors like condensin play key roles in this process, it is unclear how chromosome assembly proceeds as molecular events of nucleosomes in living cells and how condensins act on nucleosomes to organize chromosomes. To approach these questions, we investigate nucleosome behavior during mitosis of living human cells using single-nucleosome tracking, combined with rapid-protein depletion technology and computational modeling. Our results show that local nucleosome motion becomes increasingly constrained during mitotic chromosome assembly, which is functionally distinct from condensed apoptotic chromatin. Condensins act as molecular crosslinkers, locally constraining nucleosomes to organize chromosomes. Additionally, nucleosome-nucleosome interactions via histone tails constrain and compact whole chromosomes. Our findings elucidate the physical nature of the chromosome assembly process during mitosis.
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Affiliation(s)
- Kayo Hibino
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Yuji Sakai
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Toyoaki Natsume
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masa A Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Masato T Kanemaki
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
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18
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Lai Y, Lin Y. Biological functions and therapeutic potential of CKS2 in human cancer. Front Oncol 2024; 14:1424569. [PMID: 39188686 PMCID: PMC11345170 DOI: 10.3389/fonc.2024.1424569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
The incidence of cancer is increasing worldwide and is the most common cause of death. Identification of novel cancer diagnostic and prognostic biomarkers is important for developing cancer treatment strategies and reducing mortality. Cyclin-dependent kinase subunit 2 (CKS2) is involved in cell cycle and proliferation processes, and based on these processes, CKS2 was identified as a cancer gene. CKS2 is expressed in a variety of tissues in the human body, but its abnormal expression is associated with cancer in a variety of systems. CKS2 is generally elevated in cancer, plays a role in almost all aspects of cancer biology (such as cell proliferation, invasion, metastasis, and drug resistance) through multiple mechanisms regulating certain important genes, and is associated with clinicopathological features of patients. In addition, CKS2 expression patterns are closely related to cancer type, stage and other clinical variables. Therefore, CKS2 is considered as a tool for cancer diagnosis and prognosis and may be a promising tumor biomarker and therapeutic target. This article reviews the biological function, mechanism of action and potential clinical significance of CKS2 in cancer, in order to provide a new theoretical basis for clinical molecular diagnosis, molecular targeted therapy and scientific research of cancer.
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Affiliation(s)
- Yueliang Lai
- Department of Gastroenterology, Ganzhou People’s Hospital, Ganzhou, Jiangxi, China
- The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi, China
| | - Ye Lin
- Department of Gastroenterology, Ganzhou People’s Hospital, Ganzhou, Jiangxi, China
- The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi, China
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19
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Bachmann V, Schädel P, Westhoff J, Perić M, Schömberg F, Skaltsounis AL, Höppener S, Pantsar T, Fischer D, Vilotijević I, Werz O. Bromo-substituted indirubins for inhibition of protein kinase-mediated signalling involved in inflammatory mediator release in human monocytes. Bioorg Chem 2024; 149:107470. [PMID: 38838619 DOI: 10.1016/j.bioorg.2024.107470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Targeting protein kinases that regulate signalling pathways in inflammation is an effective pharmacological approach to alleviate uncontrolled inflammatory diseases. In this context, the natural product indirubin and its 6-bromo-substituted analogue 6-bromoindirubin-3 -glycerol-oxime ether (6BIGOE; 1) were identified as potent inhibitors of glycogen synthase kinase-3β (GSK-3β). These inhibitors suppress the release of pro-inflammatory cytokines and prostaglandins (PG) from human monocytes. However, indirubin derivatives target several protein kinases such as cyclin-dependent kinases (CDKs) which has been a major concern for their application in inflammation therapy. Here, we report on a library of 13 5-bromo-substituted indirubin derivatives that have been designed to improve potency and target selectivity. Side-by-side comparison of reference compound 1 (6BIGOE) with 5-bromo derivatives revealed its isomer 2 (5BIGOE), as the most potent derivative able to supress pro-inflammatory cytokine and PG release in lipopolysaccharide-stimulated human monocytes. Analysis of protein kinase inhibition in intact monocytes, supported by our in silico findings, proposed higher selectivity of 1 for GSK-3β inhibition with lesser potency against CDKs 8 and 9. In contrast, 2 supressed the activity of these CDKs with higher effectiveness than GSK-3β, representing additional targets of indirubins within the inflammatory response. Encapsulation of 1 and 2 into polymer-based nanoparticles (NP) improved their pharmacological potential. In conclusion, the 5- and 6-brominated indirubins 1 and 2 as dual GSK-3β and CDK8/9 inhibitors represent a novel concept for intervention with inflammatory disorders.
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Affiliation(s)
- Vivien Bachmann
- Department of Pharmaceutical/ Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Patrick Schädel
- Department of Pharmaceutical/ Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Jan Westhoff
- Division of Pharmaceutical Technology and Biopharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 4, 91058 Erlangen, Germany
| | - Milica Perić
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany
| | - Fritz Schömberg
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany
| | - Alexios-Leandros Skaltsounis
- Department of Pharmacy, Division of Pharmacognosy and Natural Product Chemistry, University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece
| | - Stephanie Höppener
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Tatu Pantsar
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonrinne 3, FI-70210 Kuopio, Finland
| | - Dagmar Fischer
- Division of Pharmaceutical Technology and Biopharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 4, 91058 Erlangen, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany; FAU NeW - Research Center for New Bioactive Compounds, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Ivan Vilotijević
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany.
| | - Oliver Werz
- Department of Pharmaceutical/ Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany.
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20
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Mouery BL, Baker EM, Mei L, Wolff SC, Mills CA, Fleifel D, Mulugeta N, Herring LE, Cook JG. APC/C prevents a noncanonical order of cyclin/CDK activity to maintain CDK4/6 inhibitor-induced arrest. Proc Natl Acad Sci U S A 2024; 121:e2319574121. [PMID: 39024113 PMCID: PMC11287123 DOI: 10.1073/pnas.2319574121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/21/2024] [Indexed: 07/20/2024] Open
Abstract
Regulated cell cycle progression ensures homeostasis and prevents cancer. In proliferating cells, premature S phase entry is avoided by the E3 ubiquitin ligase anaphasepromoting complex/cyclosome (APC/C), although the APC/C substrates whose degradation restrains G1-S progression are not fully known. The APC/C is also active in arrested cells that exited the cell cycle, but it is not clear whether APC/C maintains all types of arrest. Here, by expressing the APC/C inhibitor, EMI1, we show that APC/C activity is essential to prevent S phase entry in cells arrested by pharmacological cyclin-dependent kinases 4 and 6 (CDK4/6) inhibition (Palbociclib). Thus, active protein degradation is required for arrest alongside repressed cell cycle gene expression. The mechanism of rapid and robust arrest bypass from inhibiting APC/C involves CDKs acting in an atypical order to inactivate retinoblastoma-mediated E2F repression. Inactivating APC/C first causes mitotic cyclin B accumulation which then promotes cyclin A expression. We propose that cyclin A is the key substrate for maintaining arrest because APC/C-resistant cyclin A, but not cyclin B, is sufficient to induce S phase entry. Cells bypassing arrest from CDK4/6 inhibition initiate DNA replication with severely reduced origin licensing. The simultaneous accumulation of S phase licensing inhibitors, such as cyclin A and geminin, with G1 licensing activators disrupts the normal order of G1-S progression. As a result, DNA synthesis and cell proliferation are profoundly impaired. Our findings predict that cancers with elevated EMI1 expression will tend to escape CDK4/6 inhibition into a premature, underlicensed S phase and suffer enhanced genome instability.
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Affiliation(s)
- Brandon L. Mouery
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Eliyambuya M. Baker
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10021
| | - Liu Mei
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Samuel C. Wolff
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Computational Medicine Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Christine A. Mills
- University of North Carolina Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Nebyou Mulugeta
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Laura E. Herring
- University of North Carolina Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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21
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Zhang Y, Fong KW, Mao F, Wang R, Allison DB, Napier D, He D, Liu J, Zhang Y, Chen J, Kong Y, Li C, Li G, Liu J, Li Z, Zhu H, Wang C, Liu X. Elevating PLK1 overcomes BETi resistance in prostate cancer via triggering BRD4 phosphorylation-dependent degradation in mitosis. Cell Rep 2024; 43:114431. [PMID: 38968071 PMCID: PMC11334074 DOI: 10.1016/j.celrep.2024.114431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/20/2024] [Accepted: 06/18/2024] [Indexed: 07/07/2024] Open
Abstract
Bromodomain-containing protein 4 (BRD4) has emerged as a promising therapeutic target in prostate cancer (PCa). Understanding the mechanisms of BRD4 stability could enhance the clinical response to BRD4-targeted therapy. In this study, we report that BRD4 protein levels are significantly decreased during mitosis in a PLK1-dependent manner. Mechanistically, we show that BRD4 is primarily phosphorylated at T1186 by the CDK1/cyclin B complex, recruiting PLK1 to phosphorylate BRD4 at S24/S1100, which are recognized by the APC/CCdh1 complex for proteasome pathway degradation. We find that PLK1 overexpression lowers SPOP mutation-stabilized BRD4, consequently rendering PCa cells re-sensitized to BRD4 inhibitors. Intriguingly, we report that sequential treatment of docetaxel and JQ1 resulted in significant inhibition of PCa. Collectively, the results support that PLK1-phosphorylated BRD4 triggers its degradation at M phase. Sequential treatment of docetaxel and JQ1 overcomes BRD4 accumulation-associated bromodomain and extra-terminal inhibitor (BETi) resistance, which may shed light on the development of strategies to treat PCa.
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Affiliation(s)
- Yanquan Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
| | - Ka-Wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Fengyi Mao
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Ruixin Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Derek B Allison
- Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY 40508, USA
| | - Dana Napier
- Biospecimen Procurement & Translational Pathology Shared Resource Facility, University of Kentucky, Lexington, KY 40536, USA
| | - Daheng He
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Jinpeng Liu
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Yeqing Zhang
- Department of Biology, College of Arts & Sciences, University of Kentucky, Lexington, KY 40506, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Yifan Kong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Chaohao Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Guangbing Li
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghui Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Zhiguo Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
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22
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Tanaka J, Kuwajima H, Yuki R, Nakayama Y. Simvastatin activates the spindle assembly checkpoint and causes abnormal cell division by modifying small GTPases. Cell Signal 2024; 119:111172. [PMID: 38604342 DOI: 10.1016/j.cellsig.2024.111172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Simvastatin is an inhibitor of 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase, which is a rate-limiting enzyme of the cholesterol synthesis pathway. It has been used clinically as a lipid-lowering agent to reduce low-density lipoprotein (LDL) cholesterol levels. In addition, antitumor activity has been demonstrated. Although simvastatin attenuates the prenylation of small GTPases, its effects on cell division in which small GTPases play an important role, have not been examined as a mechanism underlying its cytostatic effects. In this study, we determined its effect on cell division. Cell cycle synchronization experiments revealed a delay in mitotic progression in simvastatin-treated cells at concentrations lower than the IC50. Time-lapse imaging analysis indicated that the duration of mitosis, especially from mitotic entry to anaphase onset, was prolonged. In addition, simvastatin increased the number of cells exhibiting misoriented anaphase/telophase and bleb formation. Inhibition of the spindle assembly checkpoint (SAC) kinase Mps1 canceled the mitotic delay. Additionally, the number of cells exhibiting kinetochore localization of BubR1, an essential component of SAC, was increased, suggesting an involvement of SAC in the mitotic delay. Enhancement of F-actin formation and cell rounding at mitotic entry indicates that cortical actin dynamics were affected by simvastatin. The cholesterol removal agent methyl-β-cyclodextrin (MβCD) accelerated mitotic progression differently from simvastatin, suggesting that cholesterol loss from the plasma membrane is not involved in the mitotic delay. Of note, the small GTPase RhoA, which is a critical factor for cortical actin dynamics, exhibited upregulated expression. In addition, Rap1 was likely not geranylgeranylated. Our results demonstrate that simvastatin affects actin dynamics by modifying small GTPases, thereby activating the spindle assembly checkpoint and causing abnormal cell division.
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Affiliation(s)
- Junna Tanaka
- Laboratory of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414, Japan
| | - Hiroki Kuwajima
- Laboratory of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414, Japan
| | - Ryuzaburo Yuki
- Laboratory of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414, Japan
| | - Yuji Nakayama
- Laboratory of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414, Japan.
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23
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Giancola JB, Raines RT. Endosomolytic Peptides Enable the Cellular Delivery of Peptide Nucleic Acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599558. [PMID: 38948866 PMCID: PMC11213006 DOI: 10.1101/2024.06.18.599558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Precision genetic medicine enlists antisense oligonucleotides (ASOs) to bind to nucleic acid targets important for human disease. Peptide nucleic acids (PNAs) have many desirable attributes as ASOs but lack cellular permeability. Here, we use an assay based on the corrective splicing of an mRNA to assess the ability of synthetic peptides to deliver a functional PNA into a human cell. We find that the endosomolytic peptides L17E and L17ER 4 are highly efficacious delivery vehicles. Co-treatment of a PNA with low micromolar L17E or L17ER 4 enables robust corrective splicing in nearly all treated cells. Peptide-PNA conjugates are even more effective. These results enhance the utility of PNAs as research tools and potential therapeutic agents.
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24
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Chen Z, Wang X, Gao X, Arslanovic N, Chen K, Tyler J. Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.20.567799. [PMID: 38045243 PMCID: PMC10690177 DOI: 10.1101/2023.11.20.567799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
In response to DNA double strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR / Cas9 screen. Many of the top hits in our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G1 or G2 phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.
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Affiliation(s)
- Zulong Chen
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nina Arslanovic
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
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25
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Coscia SM, Moore AS, Thompson CP, Tirrito CF, Ostap EM, Holzbaur ELF. An interphase actin wave promotes mitochondrial content mixing and organelle homeostasis. Nat Commun 2024; 15:3793. [PMID: 38714822 PMCID: PMC11076292 DOI: 10.1038/s41467-024-48189-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 04/22/2024] [Indexed: 05/10/2024] Open
Abstract
Across the cell cycle, mitochondrial dynamics are regulated by a cycling wave of actin polymerization/depolymerization. In metaphase, this wave induces actin comet tails on mitochondria that propel these organelles to drive spatial mixing, resulting in their equitable inheritance by daughter cells. In contrast, during interphase the cycling actin wave promotes localized mitochondrial fission. Here, we identify the F-actin nucleator/elongator FMNL1 as a positive regulator of the wave. FMNL1-depleted cells exhibit decreased mitochondrial polarization, decreased mitochondrial oxygen consumption, and increased production of reactive oxygen species. Accompanying these changes is a loss of hetero-fusion of wave-fragmented mitochondria. Thus, we propose that the interphase actin wave maintains mitochondrial homeostasis by promoting mitochondrial content mixing. Finally, we investigate the mechanistic basis for the observation that the wave drives mitochondrial motility in metaphase but mitochondrial fission in interphase. Our data indicate that when the force of actin polymerization is resisted by mitochondrial tethering to microtubules, as in interphase, fission results.
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Affiliation(s)
- Stephen M Coscia
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Andrew S Moore
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Cameron P Thompson
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christian F Tirrito
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E Michael Ostap
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Erika L F Holzbaur
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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26
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Reinecke M, Brear P, Vornholz L, Berger BT, Seefried F, Wilhelm S, Samaras P, Gyenis L, Litchfield DW, Médard G, Müller S, Ruland J, Hyvönen M, Wilhelm M, Kuster B. Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Nat Chem Biol 2024; 20:577-585. [PMID: 37904048 PMCID: PMC11062922 DOI: 10.1038/s41589-023-01459-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/22/2023] [Indexed: 11/01/2023]
Abstract
Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Compounds targeting PKN3 were discovered and phosphoproteomics identified substrates that indicate target engagement in cells. We anticipate that this molecular resource will aid research in drug discovery and chemical biology.
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Affiliation(s)
- Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Larsen Vornholz
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Benedict-Tilmann Berger
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Florian Seefried
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David William Litchfield
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Jürgen Ruland
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
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27
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Shintomi K, Masahara-Negishi Y, Shima M, Tane S, Hirano T. Recombinant cyclin B-Cdk1-Suc1 capable of multi-site mitotic phosphorylation in vitro. PLoS One 2024; 19:e0299003. [PMID: 38527022 PMCID: PMC10962838 DOI: 10.1371/journal.pone.0299003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024] Open
Abstract
Cyclin-dependent kinase 1 (Cdk1) complexed with cyclin B phosphorylates multiple sites on hundreds of proteins during mitosis. However, it is not fully understood how multi-site mitotic phosphorylation by cyclin B-Cdk1 controls the structures and functions of individual substrates. Here we develop an easy-to-use protocol to express recombinant vertebrate cyclin B and Cdk1 in insect cells from a single baculovirus vector and to purify their complexes with excellent homogeneity. A series of in-vitro assays demonstrate that the recombinant cyclin B-Cdk1 can efficiently and specifically phosphorylate the SP and TP motifs in substrates. The addition of Suc1 (a Cks1 homolog in fission yeast) accelerates multi-site phosphorylation of an artificial substrate containing TP motifs. Importantly, we show that mitosis-specific multi-subunit and multi-site phosphorylation of the condensin I complex can be recapitulated in vitro using recombinant cyclin B-Cdk1-Suc1. The materials and protocols described here will pave the way for dissecting the biochemical basis of critical mitotic processes that accompany Cdk1-mediated large-scale phosphorylation.
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Affiliation(s)
- Keishi Shintomi
- Chromosome Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Yuki Masahara-Negishi
- Chromosome Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Masami Shima
- Chromosome Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Shoji Tane
- Chromosome Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
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28
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley TF, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. Nat Commun 2024; 15:1943. [PMID: 38431617 PMCID: PMC10908796 DOI: 10.1038/s41467-024-45947-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
DNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes. RTF2, like RNase H2, is essential for mammalian development and maintains normal replication speed. However, persistent RTF2 and RNase H2 at stalled replication forks prevent efficient replication restart, which is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for RTF2-dependent regulation of replication-coupled ribonucleotide removal and reveal the existence of PRIM1-mediated direct replication restart in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas J Blobel
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Tom F Wiley
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics, The Rockefeller University, New York, NY, 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA.
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29
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Locke AJ, Abou Farraj R, Tran C, Zeinali E, Mashayekhi F, Ali JYH, Glover JNM, Ismail IH. The role of RNF138 in DNA end resection is regulated by ubiquitylation and CDK phosphorylation. J Biol Chem 2024; 300:105709. [PMID: 38309501 PMCID: PMC10910129 DOI: 10.1016/j.jbc.2024.105709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/02/2024] [Accepted: 01/18/2024] [Indexed: 02/05/2024] Open
Abstract
Double-strand breaks (DSBs) are DNA lesions that pose a significant threat to genomic stability. The repair of DSBs by the homologous recombination (HR) pathway is preceded by DNA end resection, the 5' to 3' nucleolytic degradation of DNA away from the DSB. We and others previously identified a role for RNF138, a really interesting new gene finger E3 ubiquitin ligase, in stimulating DNA end resection and HR. Yet, little is known about how RNF138's function is regulated in the context of DSB repair. Here, we show that RNF138 is phosphorylated at residue T27 by cyclin-dependent kinase (CDK) activity during the S and G2 phases of the cell cycle. We also observe that RNF138 is ubiquitylated constitutively, with ubiquitylation occurring in part on residue K158 and rising during the S/G2 phases. Interestingly, RNF138 ubiquitylation decreases upon genotoxic stress. By mutating RNF138 at residues T27, K158, and the previously identified S124 ataxia telangiectasia mutated phosphorylation site (Han et al., 2016, ref. 22), we find that post-translational modifications at all three positions mediate DSB repair. Cells expressing the T27A, K158R, and S124A variants of RNF138 are impaired in DNA end resection, HR activity, and are more sensitive to ionizing radiation compared to those expressing wildtype RNF138. Our findings shed more light on how RNF138 activity is controlled by the cell during HR.
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Affiliation(s)
- Andrew J Locke
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Rabih Abou Farraj
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Caroline Tran
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Elham Zeinali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Jana Yasser Hafez Ali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada; Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
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30
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Foster J, McPhee M, Yue L, Dellaire G, Pelech S, Ridgway ND. Lipid- and phospho-regulation of CTP:Phosphocholine Cytidylyltransferase α association with nuclear lipid droplets. Mol Biol Cell 2024; 35:ar33. [PMID: 38170618 PMCID: PMC10916874 DOI: 10.1091/mbc.e23-09-0354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
Fatty acids stored in triacylglycerol-rich lipid droplets are assembled with a surface monolayer composed primarily of phosphatidylcholine (PC). Fatty acids stimulate PC synthesis by translocating CTP:phosphocholine cytidylyltransferase (CCT) α to the inner nuclear membrane, nuclear lipid droplets (nLD) and lipid associated promyelocytic leukemia (PML) structures (LAPS). Huh7 cells were used to identify how CCTα translocation onto these nuclear structures are regulated by fatty acids and phosphorylation of its serine-rich P-domain. Oleate treatment of Huh7 cells increased nLDs and LAPS that became progressively enriched in CCTα. In cells expressing the phosphatidic acid phosphatase Lipin1α or 1β, the expanded pool of nLDs and LAPS had a proportional increase in associated CCTα. In contrast, palmitate induced few nLDs and LAPS and inhibited the oleate-dependent translocation of CCTα without affecting total nLDs. Phospho-memetic or phospho-null mutations in the P-domain revealed that a 70% phosphorylation threshold, rather than site-specific phosphorylation, regulated CCTα association with nLDs and LAPS. In vitro candidate kinase and inhibitor studies in Huh7 cells identified cyclin-dependent kinase (CDK) 1 and 2 as putative P-domain kinases. In conclusion, CCTα translocation onto nLDs and LAPS is dependent on available surface area and fatty acid composition, as well as threshold phosphorylation of the P-domain potentially involving CDKs.
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Affiliation(s)
- Jason Foster
- Departments of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, and
| | - Michael McPhee
- Departments of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, and
| | - Lambert Yue
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada V6T 2B5
| | - Graham Dellaire
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Steven Pelech
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada V6T 2B5
- Kinexus Bioinformatics Corporation, Vancouver, BC, Canada V6P 6T3
| | - Neale D. Ridgway
- Departments of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, and
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31
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Espinosa-Martínez M, Alcázar-Fabra M, Landeira D. The molecular basis of cell memory in mammals: The epigenetic cycle. SCIENCE ADVANCES 2024; 10:eadl3188. [PMID: 38416817 PMCID: PMC10901381 DOI: 10.1126/sciadv.adl3188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Cell memory refers to the capacity of cells to maintain their gene expression program once the initiating environmental signal has ceased. This exceptional feature is key during the formation of mammalian organisms, and it is believed to be in part mediated by epigenetic factors that can endorse cells with the landmarks required to maintain transcriptional programs upon cell duplication. Here, we review current literature analyzing the molecular basis of epigenetic memory in mammals, with a focus on the mechanisms by which transcriptionally repressive chromatin modifications such as methylation of DNA and histone H3 are propagated through mitotic cell divisions. The emerging picture suggests that cellular memory is supported by an epigenetic cycle in which reversible activities carried out by epigenetic regulators in coordination with cell cycle transition create a multiphasic system that can accommodate both maintenance of cell identity and cell differentiation in proliferating stem cell populations.
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Affiliation(s)
- Mencía Espinosa-Martínez
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - María Alcázar-Fabra
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
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32
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Kang X, Chen H, Zhou Z, Tu S, Cui B, Li Y, Dong S, Zhang Q, Xu Y. Targeting Cyclin-Dependent Kinase 1 Induces Apoptosis and Cell Cycle Arrest of Activated Hepatic Stellate Cells. Adv Biol (Weinh) 2024; 8:e2300403. [PMID: 38103005 DOI: 10.1002/adbi.202300403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/08/2023] [Indexed: 12/17/2023]
Abstract
Liver fibrosis is the integral process of chronic liver diseases caused by multiple etiologies and characterized by excessive deposition of extracellular matrix (ECM). During liver fibrosis, hepatic stellate cells (HSCs) transform into a highly proliferative, activated state, producing various cytokines, chemokines, and ECM. However, the precise mechanisms that license HSCs into the highly proliferative state remain unclear. Cyclin-dependent kinase 1 (CDK1) is a requisite event for the transition of the G1/S and G2/M phases in eukaryotic cells. In this study, it is demonstrated that CDK1 and its activating partners, Cyclin A2 and Cyclin B1, are upregulated in both liver fibrosis/cirrhosis patient specimens and the murine hepatic fibrosis models, especially in activated HSCs. In vitro, CDK1 is upregulated in spontaneously activated HSCs, and inhibiting CDK1 with specific small-molecule inhibitors (CGP74514A, RO-3306, or Purvalanol A) orshort hairpin RNAs (shRNAs) resulted in HSC apoptosis and cell cycle arrest by regulating Survivin expression. Above all, it is illustrated that increased CDK1 expression licenses the HSCs into a highly proliferative state and can serve as a potential therapeutic target in liver fibrosis.
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Affiliation(s)
- Xinmei Kang
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Huaxin Chen
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Zhuowei Zhou
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Silin Tu
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Bo Cui
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Yanli Li
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Shuai Dong
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Qi Zhang
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
- Cell-gene Therapy Translational Medicine Research Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Yan Xu
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
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33
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Musa M, Abid M, Bradshaw TD, Boocock DJ, Coveney C, Argent SP, Woodward S. Probing the Mechanism of Action of Bis(phenolato) Amine (ONO Donor Set) Titanium(IV) Anticancer Agents. J Med Chem 2024; 67:2732-2744. [PMID: 38331433 PMCID: PMC10895680 DOI: 10.1021/acs.jmedchem.3c01874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
The need for anticancer therapies that overcome metallodrug resistance while minimizing adverse toxicities is targeted, herein, using titanium coordination complexes. Octahedral titanium(IV) trans,mer-[Ti{R1N(CH2-2-MeO-4-R1-C6H2)2}2] [R1 = Et, allyl, n-Pr, CHO, F, CH2(morpholino), the latter from the formyl derivative; R2 = Me, Et; not all combinations] are attained from Mannich reactions of commercial 2-methoxyphenols (27-74% overall yield, 2 steps). These crystalline (four X-ray structures) Ti(IV)-complexes are active against MCF-7, HCT-116, HT-29, PANC-1, and MDA-MB-468 cancer cell lines (GI50 = 0.5-38 μM). Their activity and cancer selectivity (vs nontumor MRC-5 cells) typically exceeds that of cisplatin (up to 16-fold). Proteomic analysis (in MCF-7) supported by other studies (G2/M cell cycle arrest, ROS generation, γH2AX production, caspase activation, annexin positivity, western blot, and kinase screens in MCF-7 and HCT-116) suggest apoptosis elicited by more than one mechanism of action. Comparison of these data to the modes of action proposed for salan Ti(IV) complexes is made.
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Affiliation(s)
- Mustapha Musa
- GSK
Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham, Triumph Road, Nottingham NG7 2TU, U.K.
| | - Mohammed Abid
- Department
of Chemistry, College of Science, University
of Anbar, Anbarshire 31001, Iraq
| | - Tracey D. Bradshaw
- BDI,
School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - David J. Boocock
- School
of Science and Technology, Nottingham Trent
University, Clifton, Nottingham NG11 8NS, U.K.
| | - Clare Coveney
- School
of Science and Technology, Nottingham Trent
University, Clifton, Nottingham NG11 8NS, U.K.
| | - Stephen P. Argent
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Simon Woodward
- GSK
Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham, Triumph Road, Nottingham NG7 2TU, U.K.
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34
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Joshi JN, Lerner AD, Scallo F, Grumet AN, Matteson P, Millonig JH, Valvezan AJ. mTORC1 activity oscillates throughout the cell cycle promoting mitotic entry and differentially influencing autophagy induction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579216. [PMID: 38370755 PMCID: PMC10871213 DOI: 10.1101/2024.02.06.579216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a master metabolic regulator that stimulates anabolic cell growth while suppressing catabolic processes such as autophagy. mTORC1 is active in most, if not all, proliferating eukaryotic cells. However, it remains unclear whether and how mTORC1 activity changes from one cell cycle phase to another. Here we tracked mTORC1 activity through the complete cell cycle and uncover oscillations in its activity. We find that mTORC1 activity peaks in S and G2, and is lowest in mitosis and G1. We further demonstrate that multiple mechanisms are involved in controlling this oscillation. The interphase oscillation is mediated through the TSC complex, an upstream negative regulator of mTORC1, but is independent of major known regulatory inputs to the TSC complex, including Akt, Mek/Erk, and CDK4/6 signaling. By contrast, suppression of mTORC1 activity in mitosis does not require the TSC complex, and instead involves CDK1-dependent control of the subcellular localization of mTORC1 itself. Functionally, we find that in addition to its well-established role in promoting progression through G1, mTORC1 also promotes progression through S and G2, and is important for satisfying the Wee1- and Chk1- dependent G2/M checkpoint to allow entry into mitosis. We also find that low mTORC1 activity in G1 sensitizes cells to autophagy induction in response to partial mTORC1 inhibition or reduced nutrient levels. Together these findings demonstrate that mTORC1 is differentially regulated throughout the cell cycle, with important phase-specific functional consequences in proliferating cells.
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Affiliation(s)
- Jay N. Joshi
- Molecular Biosciences Program, Rutgers University, Piscataway, NJ, USA
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - Ariel D. Lerner
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - Frank Scallo
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
- Present affiliation: Yale School of Medicine, New Haven, CT, USA
| | | | - Paul Matteson
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - James H. Millonig
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Alexander J. Valvezan
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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35
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Pham AT, Mani M, Wang X, Vafabakhsh R. Multiscale biophysical analysis of nucleolus disassembly during mitosis. Proc Natl Acad Sci U S A 2024; 121:e2312250121. [PMID: 38285946 PMCID: PMC10861868 DOI: 10.1073/pnas.2312250121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/01/2024] [Indexed: 01/31/2024] Open
Abstract
During cell division, precise and regulated distribution of cellular material between daughter cells is a critical step and is governed by complex biochemical and biophysical mechanisms. To achieve this, membraneless organelles and condensates often require complete disassembly during mitosis. The biophysical principles governing the disassembly of condensates remain poorly understood. Here, we used a physical biology approach to study how physical and material properties of the nucleolus, a prominent nuclear membraneless organelle in eukaryotic cells, change during mitosis and across different scales. We found that nucleolus disassembly proceeds continuously through two distinct phases with a slow and reversible preparatory phase followed by a rapid irreversible phase that was concurrent with the nuclear envelope breakdown. We measured microscopic properties of nucleolar material including effective diffusion rates and binding affinities as well as key macroscopic properties of surface tension and bending rigidity. By incorporating these measurements into the framework of critical phenomena, we found evidence that near mitosis surface tension displays a power-law behavior as a function of biochemically modulated interaction strength. This two-step disassembly mechanism maintains structural and functional stability of nucleolus while enabling its rapid and efficient disassembly in response to cell cycle cues.
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Affiliation(s)
- An T. Pham
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL60208
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL60208
| | - Xiaozhong Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL60208
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
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36
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Naufal M, Hermawati E, Syah YM, Hidayat AT, Hidayat IW, Al-Anshori J. Structure-Activity Relationship Study and Design Strategies of Hydantoin, Thiazolidinedione, and Rhodanine-Based Kinase Inhibitors: A Two-Decade Review. ACS OMEGA 2024; 9:4186-4209. [PMID: 38313530 PMCID: PMC10832052 DOI: 10.1021/acsomega.3c04749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 02/06/2024]
Abstract
Cancer is one of the most prominent causes of the rapidly growing mortality numbers worldwide. Cancer originates from normal cells that have acquired the capability to alter their molecular, biochemical, and cellular traits. The alteration of cell signaling enzymes, such as kinases, can initiate and amplify cancer progression. As a curative method, the targeted therapy utilized small molecules' capability to inhibit kinase's cellular function. This review provides a brief history (1999-2023) of Small Molecule Kinase Inhibitors (SMKIs) discovery with their molecular perspective. Furthermore, this current review also addresses the application and the development of hydantoin, thiazolidinedione, and rhodanine-based derivatives as kinase inhibitors toward several subclasses (EGFR, PI3K, VEGFR, Pim, c-Met, CDK, IGFR, and ERK) accompanied by their structure-activity relationship study and their molecular interactions. The present work summarizes and compiles all the important structural information essential for developing hydantoin, thiazolidinedione, and rhodanine-based kinase inhibitors to improve their potency in the future.
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Affiliation(s)
- Muhammad Naufal
- Department
of Chemistry, Padjadjaran University, Jalan Raya Bandung-Sumedang Km.
21, Jatinangor, Sumedang 45363, Indonesia
| | - Elvira Hermawati
- Department
of Chemistry, Bandung Institute of Technology, Jalan Ganesha Nomor 10, Bandung, Jawa Barat 40132, Indonesia
| | - Yana Maolana Syah
- Department
of Chemistry, Bandung Institute of Technology, Jalan Ganesha Nomor 10, Bandung, Jawa Barat 40132, Indonesia
| | - Ace Tatang Hidayat
- Department
of Chemistry, Padjadjaran University, Jalan Raya Bandung-Sumedang Km.
21, Jatinangor, Sumedang 45363, Indonesia
| | - Ika Wiani Hidayat
- Department
of Chemistry, Padjadjaran University, Jalan Raya Bandung-Sumedang Km.
21, Jatinangor, Sumedang 45363, Indonesia
| | - Jamaludin Al-Anshori
- Department
of Chemistry, Padjadjaran University, Jalan Raya Bandung-Sumedang Km.
21, Jatinangor, Sumedang 45363, Indonesia
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37
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Tanaka T, Miyakoshi Y, Kobayashi Y, Xiaolong S, Daiyang Y, Ochi H, Sato S, Kato T, Yoshii T, Okawa A, Kaldis P, Inose H. Regulation of Osteoblast to Osteocyte Differentiation by Cyclin-Dependent Kinase-1. Adv Biol (Weinh) 2023; 7:e2300136. [PMID: 37424388 DOI: 10.1002/adbi.202300136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/16/2023] [Indexed: 07/11/2023]
Abstract
Osteocytes have recently been identified as a new regulator of bone remodeling, but the detailed mechanism of their differentiation from osteoblasts remains unclear. The purpose of this study is to identify cell cycle regulators involved in the differentiation of osteoblasts into osteocytes and determine their physiological significance. The study uses IDG-SW3 cells as a model for the differentiation from osteoblasts to osteocytes. Among the major cyclin-dependent kinases (Cdks), Cdk1 is most abundantly expressed in IDG-SW3 cells, and its expression is down-regulated during differentiation into osteocytes. Inhibition of CDK1 activity reduces IDG-SW3 cell proliferation and differentiation into osteocytes. Osteocyte and Osteoblast-specific Cdk1 knockout in mice (Dmp1-Cdk1KO ) results in trabecular bone loss. Pthlh expression increases during differentiation, but inhibiting CDK1 activity reduces Pthlh expression. Parathyroid hormone-related protein concentration is reduced in the bone marrow of Dmp1-Cdk1KO mice. Four weeks of Parathyroid hormone administration partially recovers the trabecular bone loss in Dmp1-Cdk1KO mice. These results demonstrate that Cdk1 plays an essential role in the differentiation from osteoblast to osteocyte and the acquisition and maintenance of bone mass. The findings contribute to a better understanding of the mechanisms of bone mass regulation and can help develop efficient therapeutic strategies for osteoporosis treatment.
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Affiliation(s)
- Tomoyuki Tanaka
- Department of Orthopaedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
- Department of Orthopaedic Surgery, Dokkyo Medical University Saitama Medical Center, 2-1-50 Minamikoshigaya, Koshigaya-shi, Saitama, 343-8555, Japan
| | - Yuri Miyakoshi
- Department of Orthopaedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Yutaka Kobayashi
- Department of Orthopaedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Sun Xiaolong
- Department of Orthopaedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Yu Daiyang
- Department of Orthopaedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Hiroki Ochi
- Department of Rehabilitation for Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, 4-1 Namiki, Tokorozawa, Saitama, 359-8555, Japan
| | - Shingo Sato
- Center for Innovative Cancer Treatment, Tokyo Medical and Dental University Hospital, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Tsuyoshi Kato
- Department of Orthopaedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Toshitaka Yoshii
- Department of Orthopaedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Atsushi Okawa
- Department of Orthopaedics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Philipp Kaldis
- Department of Clinical Sciences, Lund University, Clinical Research Centre (CRC) Box 50332, Malmö, SE-202 13, Sweden
- Lund University Diabetes Centre (LUDC), Lund University, Malmö, SE-202 13, Sweden
| | - Hiroyuki Inose
- Department of Orthopaedic Surgery, Dokkyo Medical University Saitama Medical Center, 2-1-50 Minamikoshigaya, Koshigaya-shi, Saitama, 343-8555, Japan
- Department of Orthopedic and Trauma Research, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
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Nair VM, Sabu AS, Hussain A, Kombarakkaran DP, Lakshmi RB, Manna TK. E3-ubiquitin ligase, FBXW7 regulates mitotic progression by targeting BubR1 for ubiquitin-mediated degradation. Cell Mol Life Sci 2023; 80:374. [PMID: 38008853 PMCID: PMC11072012 DOI: 10.1007/s00018-023-05019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/28/2023]
Abstract
Faithful chromosome segregation requires correct attachment of kinetochores with the spindle microtubules. Erroneously-attached kinetochores recruit proteins to activate Spindle assembly checkpoint (SAC), which senses the errors and signals cells to delay anaphase progression for error correction. Temporal control of the levels of SAC activating-proteins is critical for checkpoint activation and silencing, but its mechanism is not fully understood. Here, we show that E3 ubiquitin ligase, SCF-FBXW7 targets BubR1 for ubiquitin-mediated degradation and thereby controls SAC in human cells. Depletion of FBXW7 results in prolonged metaphase arrest with increased stabilization of BubR1 at kinetochores. Similar kinetochore stabilization is also observed for BubR1-interacting protein, CENP-E. FBXW7 induced ubiquitination of both BubR1 and the BubR1-interacting kinetochore-targeting domain of CENP-E, but CENP-E domain degradation is dependent on BubR1. Interestingly, Cdk1 inhibition disrupts FBXW7-mediated BubR1 targeting and further, phospho-resistant mutation of Cdk1-targeted phosphorylation site, Thr 620 impairs BubR1-FBXW7 interaction and FBXW7-mediated BubR1 ubiquitination, supporting its role as a phosphodegron for FBXW7. The results demonstrate SCF-FBXW7 as a key regulator of spindle assembly checkpoint that controls stability of BubR1 and its associated CENP-E at kinetochores. They also support that upstream Cdk1 specific BubR1 phosphorylation signals the ligase to activate the process.
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Affiliation(s)
- Vishnu M Nair
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - Amit Santhu Sabu
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - Ahmed Hussain
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - Delvin P Kombarakkaran
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - R Bhagya Lakshmi
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - Tapas K Manna
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India.
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39
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Traband EL, Hammerlund SR, Shameem M, Narayan A, Ramana S, Tella A, Sobeck A, Shima N. Mitotic DNA Synthesis in Untransformed Human Cells Preserves Common Fragile Site Stability via a FANCD2-Driven Mechanism That Requires HELQ. J Mol Biol 2023; 435:168294. [PMID: 37777152 PMCID: PMC10839910 DOI: 10.1016/j.jmb.2023.168294] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Faithful genome duplication is a challenging task for dividing mammalian cells, particularly under replication stress where timely resolution of late replication intermediates (LRIs) becomes crucial prior to cell division. In human cancer cells, mitotic DNA repair synthesis (MiDAS) is described as a final mechanism for the resolution of LRIs to avoid lethal chromosome mis-segregation. RAD52-driven MiDAS achieves this mission in part by generating gaps/breaks on metaphase chromosomes, which preferentially occur at common fragile sites (CFS). We previously demonstrated that a MiDAS mechanism also exists in untransformed and primary human cells, which is RAD52 independent but requires FANCD2. However, the properties of this form of MiDAS are not well understood. Here, we report that FANCD2-driven MiDAS in untransformed human cells: 1) requires a prerequisite step of FANCD2 mono-ubiquitination by a subset of Fanconi anemia (FA) proteins, 2) primarily acts to preserve CFS stability but not to prevent chromosome mis-segregation, and 3) depends on HELQ, which potentially functions at an early step. Hence, FANCD2-driven MiDAS in untransformed cells is built to protect CFS stability, whereas RAD52-driven MiDAS in cancer cells is likely adapted to prevent chromosome mis-segregation at the cost of CFS expression. Notably, we also identified a novel form of MiDAS, which surfaces to function when FANCD2 is absent in untransformed cells. Our findings substantiate the complex nature of MiDAS and a link between its deficiencies and the pathogenesis of FA, a human genetic disease.
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Affiliation(s)
- Emma L Traband
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Sarah R Hammerlund
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Mohammad Shameem
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Ananya Narayan
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Sanjiv Ramana
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Anika Tella
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Alexandra Sobeck
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, Minneapolis, MN 55455, USA
| | - Naoko Shima
- Department of Genetics, Cell Biology and Development, Medical School, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, Minneapolis, MN 55455, USA.
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Mouery BL, Baker EM, Mills CA, Herring LE, Fleifel D, Cook JG. APC/C prevents non-canonical order of cyclin/CDK activity to maintain CDK4/6 inhibitor-induced arrest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566394. [PMID: 37986787 PMCID: PMC10659421 DOI: 10.1101/2023.11.09.566394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Regulated cell cycle progression ensures homeostasis and prevents cancer. In proliferating cells, premature S phase entry is avoided by the E3 ubiquitin ligase APC/C (anaphase promoting complex/cyclosome), although the APC/C substrates whose degradation restrains G1-S progression are not fully known. The APC/C is also active in arrested cells that exited the cell cycle, but it is not clear if APC/C maintains all types of arrest. Here by expressing the APC/C inhibitor, EMI1, we show that APC/C activity is essential to prevent S phase entry in cells arrested by pharmacological CDK4/6 inhibition (Palbociclib). Thus, active protein degradation is required for arrest alongside repressed cell cycle gene expression. The mechanism of rapid and robust arrest bypass from inhibiting APC/C involves cyclin-dependent kinases acting in an atypical order to inactivate RB-mediated E2F repression. Inactivating APC/C first causes mitotic cyclin B accumulation which then promotes cyclin A expression. We propose that cyclin A is the key substrate for maintaining arrest because APC/C-resistant cyclin A, but not cyclin B, is sufficient to induce S phase entry. Cells bypassing arrest from CDK4/6 inhibition initiate DNA replication with severely reduced origin licensing. The simultaneous accumulation of S phase licensing inhibitors, such as cyclin A and geminin, with G1 licensing activators disrupts the normal order of G1-S progression. As a result, DNA synthesis and cell proliferation are profoundly impaired. Our findings predict that cancers with elevated EMI1 expression will tend to escape CDK4/6 inhibition into a premature, underlicensed S phase and suffer enhanced genome instability.
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Affiliation(s)
- Brandon L Mouery
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Eliyambuya M Baker
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Christine A Mills
- UNC Proteomics Core Facility, Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
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41
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Massacci G, Perfetto L, Sacco F. The Cyclin-dependent kinase 1: more than a cell cycle regulator. Br J Cancer 2023; 129:1707-1716. [PMID: 37898722 PMCID: PMC10667339 DOI: 10.1038/s41416-023-02468-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/26/2023] [Accepted: 10/13/2023] [Indexed: 10/30/2023] Open
Abstract
The Cyclin-dependent kinase 1, as a serine/threonine protein kinase, is more than a cell cycle regulator as it was originally identified. During the last decade, it has been shown to carry out versatile functions during the last decade. From cell cycle control to gene expression regulation and apoptosis, CDK1 is intimately involved in many cellular events that are vital for cell survival. Here, we provide a comprehensive catalogue of the CDK1 upstream regulators and substrates, describing how this kinase is implicated in the control of key 'cell cycle-unrelated' biological processes. Finally, we describe how deregulation of CDK1 expression and activation has been closely associated with cancer progression and drug resistance.
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Affiliation(s)
- Giorgia Massacci
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Livia Perfetto
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy.
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42
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Adhikary U, Paulo JA, Godes M, Roychoudhury S, Prew MS, Ben-Nun Y, Yu EW, Budhraja A, Opferman JT, Chowdhury D, Gygi SP, Walensky LD. Targeting MCL-1 triggers DNA damage and an anti-proliferative response independent from apoptosis induction. Cell Rep 2023; 42:113176. [PMID: 37773750 PMCID: PMC10787359 DOI: 10.1016/j.celrep.2023.113176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 07/13/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023] Open
Abstract
MCL-1 is a high-priority target due to its dominant role in the pathogenesis and chemoresistance of cancer, yet clinical trials of MCL-1 inhibitors are revealing toxic side effects. MCL-1 biology is complex, extending beyond apoptotic regulation and confounded by its multiple isoforms, its domains of unresolved structure and function, and challenges in distinguishing noncanonical activities from the apoptotic response. We find that, in the presence or absence of an intact mitochondrial apoptotic pathway, genetic deletion or pharmacologic targeting of MCL-1 induces DNA damage and retards cell proliferation. Indeed, the cancer cell susceptibility profile of MCL-1 inhibitors better matches that of anti-proliferative than pro-apoptotic drugs, expanding their potential therapeutic applications, including synergistic combinations, but heightening therapeutic window concerns. Proteomic profiling provides a resource for mechanistic dissection and reveals the minichromosome maintenance DNA helicase as an interacting nuclear protein complex that links MCL-1 to the regulation of DNA integrity and cell-cycle progression.
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Affiliation(s)
- Utsarga Adhikary
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marina Godes
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Michelle S Prew
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yael Ben-Nun
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ellen W Yu
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amit Budhraja
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Joseph T Opferman
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Loren D Walensky
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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43
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Quadri R, Rotondo G, Sertic S, Pozzi S, dell’Oca MC, Guerrini L, Muzi-Falconi M. A Haspin-ARHGAP11A axis regulates epithelial morphogenesis through Rho-ROCK dependent modulation of LIMK1-Cofilin. iScience 2023; 26:108011. [PMID: 37841592 PMCID: PMC10570125 DOI: 10.1016/j.isci.2023.108011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/20/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
Throughout mitosis, a plethora of processes must be efficiently concerted to ensure cell proliferation and tissue functionality. The mitotic spindle does not only mediate chromosome segregation, but also defines the axis of cellular division, thus determining tissue morphology. Functional spindle orientation relies on precise actin dynamics, shaped in mitosis by the LIMK1-Cofilin axis. The kinase Haspin acts as a guardian of faithful chromosome segregation that ensures amphitelic chromosome attachment and prevents unscheduled cohesin cleavage. Here, we report an unprecedented role for Haspin in the determination of spindle orientation in mitosis. We show that, during mitosis, Haspin regulates Rho-ROCK activity through ARHGAP11A, a poorly characterized GAP, and that ROCK is in turn responsible for the mitotic activation of LIMK1 and stabilization of the actin cytoskeleton, thus supporting a functional spindle orientation. By exploiting 3D cell cultures, we show that this pathway is pivotal for the establishment of a morphologically functional tissue.
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Affiliation(s)
- Roberto Quadri
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Giuseppe Rotondo
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Sarah Sertic
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Sara Pozzi
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | | | - Luisa Guerrini
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Marco Muzi-Falconi
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
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44
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Knoblochova L, Duricek T, Vaskovicova M, Zorzompokou C, Rayova D, Ferencova I, Baran V, Schultz RM, Hoffmann ER, Drutovic D. CHK1-CDC25A-CDK1 regulate cell cycle progression and protect genome integrity in early mouse embryos. EMBO Rep 2023; 24:e56530. [PMID: 37694680 PMCID: PMC10561370 DOI: 10.15252/embr.202256530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
After fertilization, remodeling of the oocyte and sperm genomes is essential to convert these highly differentiated and transcriptionally quiescent cells into early cleavage-stage blastomeres that are transcriptionally active and totipotent. This developmental transition is accompanied by cell cycle adaptation, such as lengthening or shortening of the gap phases G1 and G2. However, regulation of these cell cycle changes is poorly understood, especially in mammals. Checkpoint kinase 1 (CHK1) is a protein kinase that regulates cell cycle progression in somatic cells. Here, we show that CHK1 regulates cell cycle progression in early mouse embryos by restraining CDK1 kinase activity due to CDC25A phosphatase degradation. CHK1 kinase also ensures the long G2 phase needed for genome activation and reprogramming gene expression in two-cell stage mouse embryos. Finally, Chk1 depletion leads to DNA damage and chromosome segregation errors that result in aneuploidy and infertility.
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Affiliation(s)
- Lucie Knoblochova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomas Duricek
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Michaela Vaskovicova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Chrysoula Zorzompokou
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Diana Rayova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Ivana Ferencova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Vladimir Baran
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of SciencesKosiceSlovakia
| | - Richard M Schultz
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCAUSA
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - David Drutovic
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
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45
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Dwivedi D, Harry D, Meraldi P. Mild replication stress causes premature centriole disengagement via a sub-critical Plk1 activity under the control of ATR-Chk1. Nat Commun 2023; 14:6088. [PMID: 37773176 PMCID: PMC10541884 DOI: 10.1038/s41467-023-41753-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
A tight synchrony between the DNA and centrosome cycle is essential for genomic integrity. Centriole disengagement, which licenses centrosomes for duplication, occurs normally during mitotic exit. We recently demonstrated that mild DNA replication stress typically seen in cancer cells causes premature centriole disengagement in untransformed mitotic human cells, leading to transient multipolar spindles that favour chromosome missegregation. How mild replication stress accelerates the centrosome cycle at the molecular level remained, however, unclear. Using ultrastructure expansion microscopy, we show that mild replication stress induces premature centriole disengagement already in G2 via the ATR-Chk1 axis of the DNA damage repair pathway. This results in a sub-critical Plk1 kinase activity that primes the pericentriolar matrix for Separase-dependent disassembly but is insufficient for rapid mitotic entry, causing premature centriole disengagement in G2. We postulate that the differential requirement of Plk1 activity for the DNA and centrosome cycles explains how mild replication stress disrupts the synchrony between both processes and contributes to genomic instability.
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Affiliation(s)
- Devashish Dwivedi
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Geneva, Switzerland
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Geneva, Switzerland
| | - Daniela Harry
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Geneva, Switzerland
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Geneva, Switzerland
| | - Patrick Meraldi
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Geneva, Switzerland.
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Geneva, Switzerland.
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46
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Pham AT, Mani M, Wang XA, Vafabakhsh R. The Physical Biology of Nucleolus Disassembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559731. [PMID: 37808669 PMCID: PMC10557732 DOI: 10.1101/2023.09.27.559731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
During cell division, precise and regulated distribution of cellular material between daughter cells is a critical step and is governed by complex biochemical and biophysical mechanisms. To achieve this, membraneless organelles and condensates often require complete disassembly during mitosis. The biophysical principles governing the disassembly of condensates remain poorly understood. Here, we used a physical biology approach to study how physical and material properties of the nucleolus, a prominent nuclear membraneless organelle in eukaryotic cells, change during mitosis and across different scales. We found that nucleolus disassembly proceeds continuously through two distinct phases with a slow and reversible preparatory phase followed by a rapid irreversible phase that was concurrent with the nuclear envelope breakdown. We measured microscopic properties of nucleolar material including effective diffusion rates and binding affinities as well as key macroscopic properties of surface tension and bending rigidity. By incorporating these measurements into the framework of critical phenomena, we found evidence that near mitosis surface tension displays a power-law behavior as a function of biochemically modulated interaction strength. This two-step disassembly mechanism, which maintains structural and functional stability of nucleolus while allowing for its rapid and efficient disassembly in response to cell cycle cues, may be a universal design principle for the disassembly of other biomolecular condensates.
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Affiliation(s)
- An T. Pham
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Xiaozhong A. Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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47
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Nagasaka K, Davidson IF, Stocsits RR, Tang W, Wutz G, Batty P, Panarotto M, Litos G, Schleiffer A, Gerlich DW, Peters JM. Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms. Mol Cell 2023; 83:3049-3063.e6. [PMID: 37591243 DOI: 10.1016/j.molcel.2023.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 05/28/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
Cohesin connects CTCF-binding sites and other genomic loci in cis to form chromatin loops and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here, we describe a cohesin hinge mutant that can extrude DNA into loops but is unable to mediate cohesion in human cells. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin's cohesion and loop extrusion activities can be partially separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wild-type cohesin. This suggests that cohesion establishment and cohesin's interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.
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Affiliation(s)
- Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Melanie Panarotto
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Gabriele Litos
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria.
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48
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Capece M, Tessari A, Mills J, Vinciguerra GLR, Louke D, Lin C, McElwain BK, Miles WO, Coppola V, Davies AE, Palmieri D, Croce CM. A novel auxin-inducible degron system for rapid, cell cycle-specific targeted proteolysis. Cell Death Differ 2023; 30:2078-2091. [PMID: 37537305 PMCID: PMC10482871 DOI: 10.1038/s41418-023-01191-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/02/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
The discrimination of protein biological functions in different phases of the cell cycle is limited by the lack of experimental approaches that do not require pre-treatment with compounds affecting the cell cycle progression. Therefore, potential cycle-specific biological functions of a protein of interest could be biased by the effects of cell treatments. The OsTIR1/auxin-inducible degron (AID) system allows "on demand" selective and reversible protein degradation upon exposure to the phytohormone auxin. In the current format, this technology does not allow to study the effect of acute protein depletion selectively in one phase of the cell cycle, as auxin similarly affects all the treated cells irrespectively of their proliferation status. Therefore, the AID system requires coupling with cell synchronization techniques, which can alter the basal biological status of the studied cell population, as with previously available approaches. Here, we introduce a new AID system to Regulate OsTIR1 Levels based on the Cell Cycle Status (ROLECCS system), which induces proteolysis of both exogenously transfected and endogenous gene-edited targets in specific phases of the cell cycle. We validated the ROLECCS technology by down regulating the protein levels of TP53, one of the most studied tumor suppressor genes, with a widely known role in cell cycle progression. By using our novel tool, we observed that TP53 degradation is associated with increased number of micronuclei, and this phenotype is specifically achieved when TP53 is lost in S/G2/M phases of the cell cycle, but not in G1. Therefore, we propose the use of the ROLECCS system as a new improved way of studying the differential roles that target proteins may have in specific phases of the cell cycle.
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Affiliation(s)
- Marina Capece
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Anna Tessari
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Joseph Mills
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Gian Luca Rampioni Vinciguerra
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Darian Louke
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Bryan K McElwain
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Wayne O Miles
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
| | - Alexander E Davies
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, 43210, Columbus, OH, USA
| | - Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA.
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
- Gene Editing Shared Resource, The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 43210, Columbus, OH, USA.
- The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, 43210, Columbus, OH, USA.
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49
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Brown VE, Moore SL, Chen M, House N, Ramsden P, Wu HJ, Ribich S, Grassian AR, Choi YJ. CDK2 regulates collapsed replication fork repair in CCNE1-amplified ovarian cancer cells via homologous recombination. NAR Cancer 2023; 5:zcad039. [PMID: 37519629 PMCID: PMC10373114 DOI: 10.1093/narcan/zcad039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/22/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
CCNE1 amplification is a common alteration in high-grade serous ovarian cancer and occurs in 15-20% of these tumors. These amplifications are mutually exclusive with homologous recombination deficiency, and, as they have intact homologous recombination, are intrinsically resistant to poly (ADP-ribose) polymerase inhibitors or chemotherapy agents. Understanding the molecular mechanisms that lead to this mutual exclusivity may reveal therapeutic vulnerabilities that could be leveraged in the clinic in this still underserved patient population. Here, we demonstrate that CCNE1-amplified high-grade serous ovarian cancer cells rely on homologous recombination to repair collapsed replication forks. Cyclin-dependent kinase 2, the canonical partner of cyclin E1, uniquely regulates homologous recombination in this genetic context, and as such cyclin-dependent kinase 2 inhibition synergizes with DNA damaging agents in vitro and in vivo. We demonstrate that combining a selective cyclin-dependent kinase 2 inhibitor with a DNA damaging agent could be a powerful tool in the clinic for high-grade serous ovarian cancer.
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Affiliation(s)
- Victoria E Brown
- To whom correspondence should be addressed. Tel: +1 617 374 7580;
| | - Sydney L Moore
- Blueprint Medicines, Cambridge, MA 02139, USA
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Maxine Chen
- Blueprint Medicines, Cambridge, MA 02139, USA
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50
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Benada J, Bulanova D, Azzoni V, Petrosius V, Ghazanfar S, Wennerberg K, Sørensen C. Synthetic lethal interaction between WEE1 and PKMYT1 is a target for multiple low-dose treatment of high-grade serous ovarian carcinoma. NAR Cancer 2023; 5:zcad029. [PMID: 37325550 PMCID: PMC10262308 DOI: 10.1093/narcan/zcad029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Ovarian cancer is driven by genetic alterations that necessitate protective DNA damage and replication stress responses through cell cycle control and genome maintenance. This creates specific vulnerabilities that may be exploited therapeutically. WEE1 kinase is a key cell cycle control kinase, and it has emerged as a promising cancer therapy target. However, adverse effects have limited its clinical progress, especially when tested in combination with chemotherapies. A strong genetic interaction between WEE1 and PKMYT1 led us to hypothesize that a multiple low-dose approach utilizing joint WEE1 and PKMYT1 inhibition would allow exploitation of the synthetic lethality. We found that the combination of WEE1 and PKMYT1 inhibition exhibited synergistic effects in eradicating ovarian cancer cells and organoid models at a low dose. The WEE1 and PKMYT1 inhibition synergistically promoted CDK activation. Furthermore, the combined treatment exacerbated DNA replication stress and replication catastrophe, leading to increase of the genomic instability and inflammatory STAT1 signalling activation. These findings suggest a new multiple low-dose approach to harness the potency of WEE1 inhibition through the synthetic lethal interaction with PKMYT1 that may contribute to the development of new treatments for ovarian cancer.
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Affiliation(s)
- Jan Benada
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Daria Bulanova
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Violette Azzoni
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Valdemaras Petrosius
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kgs Lyngby, Denmark
| | - Saba Ghazanfar
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Krister Wennerberg
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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